in the book chapter 9
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The story next returns to Dantes in prison. Dantes has lost hope and decides to commit suicide by starvation. THe dark cloud represents this.
Are you sure you're asking about Dantes here? He was jailed in the previous chapter, and the only darkening cloud I find mentioned is Villefort's brow;
“Ah, it is really a serious matter, then?” asked the marquis, remarkingthe cloud on Villefort’s brow. Chapter 9